I wanted to give those interested an updated about my efforts with Moteino MEGA (atmega1284p based Moteino). The issues are now apparently resolved and the atmega1284P is playing nicely with the RFM69 radios and the Windbond FLASH chips I am using and I am looking forward to making the first batch of MEGAs in the near future. It was mainly a SPI timing issue and the 1284P core. I was also able to rewrite DualOptiboot based on Optiboot V5.0, and can confirm that wireless programming is working on the 1284P, I will post the updated bootloader soon. There will be minor but important updates to the RFM69 and SPIFlash libraries. I will release all these in the near future along with the MEGA and its own Moteino MEGA Arduino core. Hopefully this will be a useful and stable platform for those in need of more GPIO and the extra features of the larger atmega1284p microcontroller.